Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?

Understanding why some species have more genetic diversity than others is central to the study of ecology and evolution, and carries potentially important implications for conservation biology. Yet not only does this question remain unresolved, it has largely fallen into disregard. With the rapid decrease in sequencing costs, we argue that it is time to revive it.</p

Malaria protection due to sickle haemoglobin depends on parasite genotype.

Host genetic factors can confer resistance against malaria1, raising the question of whether this has led to evolutionary adaptation of parasite populations. Here we searched for association between candidate host and parasite genetic variants in 3,346 Gambian and Kenyan children with severe malaria caused by Plasmodium falciparum. We identified a strong association between sickle haemoglobin (HbS) in the host and three regions of the parasite genome, which is not explained by population structure or other covariates, and which is replicated in additional samples. The HbS-associated alleles include nonsynonymous variants in the gene for the acyl-CoA synthetase family member2-4 PfACS8 on chromosome 2, in a second region of chromosome 2, and in a region containing structural variation on chromosome 11. The alleles are in strong linkage disequilibrium and have frequencies that covary with the frequency of HbS across populations, in particular being much more common in Africa than other parts of the world. The estimated protective effect of HbS against severe malaria, as determined by comparison of cases with population controls, varies greatly according to the parasite genotype at these three loci. These findings open up a new avenue of enquiry into the biological and epidemiological significance of the HbS-associated polymorphisms in the parasite genome and the evolutionary forces that have led to their high frequency and strong linkage disequilibrium in African P. falciparum populations

Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?

Understanding why some species have more genetic diversity than others is central to the study of ecology and evolution, and carries potentially important implications for conservation biology. Yet not only does this question remain unresolved, it has largely fallen into disregard. With the rapid decrease in sequencing costs, we argue that it is time to revive it

Data from: Stable recombination hotspots in birds

The DNA-binding protein PRDM9 has a critical role in specifying meiotic recombination hotspots in mice and apes, but it appears to be absent from other vertebrate species, including birds. To study the evolution and determinants of recombination in species lacking the gene that encodes PRDM9, we inferred fine-scale genetic maps from population resequencing data for two bird species: the zebra finch, Taeniopygia guttata, and the long-tailed finch, Poephila acuticauda. We found that both species have recombination hotspots, which are enriched near functional genomic elements. Unlike in mice and apes, most hotspots are shared between the two species, and their conservation seems to extend over tens of millions of years. These observations suggest that in the absence of PRDM9, recombination targets functional features that both enable access to the genome and constrain its evolution

Multiple Instances of Ancient Balancing Selection Shared Between Humans and Chimpanzees

Instances in which natural selection maintains genetic variation in a population over millions of years are thought to be extremely rare. We conducted a genome-wide scan for long-lived balancing selection by looking for combinations of SNPs shared between humans and chimpanzees. In addition to the major histocompatibility complex, we identified 125 regions in which the same haplotypes are segregating in the two species, all but two of which are noncoding. In six cases, there is evidence for an ancestral polymorphism that persisted to the present in humans and chimpanzees. Regions with shared haplotypes are significantly enriched for membrane glycoproteins, and a similar trend is seen among shared coding polymorphisms. These findings indicate that ancient balancing selection has shaped human variation and point to genes involved in host-pathogen interactions as common targets

Autosomal nucleotide diversity levels across species, grouped by phylum.

<p>Diversity estimates for each species are the same as in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001388#pbio-1001388-g001" target="_blank">Figure 1</a>; here they are ordered within phylum, and phyla are presented in order of their median diversity levels. Within Chordata, open circles indicate mammals, and within Arthropoda, they denote <i>Drosophila</i> species. We note that the three most diverse chordates are all invertebrate sea squirts. In panel (A), estimates are colored by the phylum to which each species belongs and horizontal bars mark the median estimate for each phylum; for Magnoliophyta, a dashed line marks the median for selfing species (open circles) and a solid line marks the median for outcrossing species. (We do not provide <i>p</i> values for comparisons because of the lack of phylogenetic independence.) Crosses denote estimates for individual populations and are shown when population structure was reported in the original study. In panel (B), estimates are colored according to whether the species lives in a terrestrial, freshwater, or marine environment (not all species are categorized). Horizontal bars indicate the median for each category within each phylum (only shown when more than two species fall in the category). The number of species in each habitat is given in parentheses in the legend.</p

Comparison of autosome and sex chromosome nucleotide diversity.

<p>The ratio of sex chromosome to autosome diversity is plotted for the 29 species in which both estimates were available from the same population(s). Colors indicate the phylum to which the species belong. Within Chordata, open circles denote mammals and open triangles birds; within Arthropoda, open circles denote <i>Drosophila</i> species. The number of species in each group is given in parentheses in the legend. Within species, crosses represent the ratio estimated from different populations, with the median of the estimates shown as a triangle (birds) or circle (all other species). Solid horizontal lines indicate the median sex chromosome to autosome ratio for arthropods and chordates, colored as in the key. The black dashed line indicates where sex chromosome diversity equals three-fourths of autosomal diversity.</p